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Yorodumi- PDB-5c1u: Crystal structure of EV71 3C Proteinase in complex with Compound Xb -
+Open data
-Basic information
Entry | Database: PDB / ID: 5c1u | |||||||||
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Title | Crystal structure of EV71 3C Proteinase in complex with Compound Xb | |||||||||
Components | 3C proteinasePicornain 3C | |||||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / HYDROLASE / CYSTEINE PROTEINASE / INHIBITOR / HYDROLASE-HYDROLASE INHIBITOR COMPLEX | |||||||||
Function / homology | Function and homology information symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / : ...symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / : / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / RNA helicase activity / induction by virus of host autophagy / RNA-directed RNA polymerase / symbiont-mediated suppression of host gene expression / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / host cell nucleus / structural molecule activity / virion attachment to host cell / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Enterovirus A71 | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 Å | |||||||||
Authors | Zhang, L. / Huang, G. / Cai, Q. / Zhao, C. / Ren, H. / Li, P. / Li, N. / Chen, S. / Li, J. / Lin, T. | |||||||||
Citation | Journal: J.Mol.Recognit. / Year: 2016 Title: Optimize the interactions at S4 with efficient inhibitors targeting 3C proteinase from enterovirus 71 Authors: Zhang, L. / Huang, G. / Cai, Q. / Zhao, C. / Tang, L. / Ren, H. / Li, P. / Li, N. / Huang, J. / Chen, X. / Guan, Y. / You, H. / Chen, S. / Li, J. / Lin, T. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5c1u.cif.gz | 95.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5c1u.ent.gz | 69.6 KB | Display | PDB format |
PDBx/mmJSON format | 5c1u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c1/5c1u ftp://data.pdbj.org/pub/pdb/validation_reports/c1/5c1u | HTTPS FTP |
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-Related structure data
Related structure data | 5c1xC 5c1yC 5c20C 4ghqS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: 0 / Auth seq-ID: 0 - 180 / Label seq-ID: 1 - 181
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-Components
#1: Protein | Mass: 21391.482 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterovirus A71 / Strain: E2004104-TW-CDC / Plasmid: PET28A / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A9XG43, picornain 3C #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.8 Å3/Da / Density % sol: 31.58 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 100MM TRIS, 25% PEG4000, 0.8M LITHIUM CHLORIDE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97931 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 7, 2011 |
Radiation | Monochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97931 Å / Relative weight: 1 |
Reflection | Resolution: 1.49→50 Å / Num. obs: 50941 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 6.2 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 13.1 |
Reflection shell | Resolution: 1.49→1.52 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.546 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4GHQ Resolution: 1.49→38.75 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.956 / SU B: 1.383 / SU ML: 0.053 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.083 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.94 Å2
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Refinement step | Cycle: LAST / Resolution: 1.49→38.75 Å
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Refine LS restraints |
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